Apparently the patch for the bug I reported in 2004 (C343-20) didn't make it into this version, despite being fixed four years ago. The glacial timescales are kind of endearing at this point.
The issue is that if you die by having a cursed ball and chain fall onto your head while descending a staircase, the screen doesn't transition to the lower level so it's not clear on which level the bones file would be generated. (Per emails from the dev team, it does get correctly generated on the lower level.) Apparently fixing this issue somehow required rewriting huge portions of the graphics engine, which probably explains the snarky comment next to the bug in the issue tracker. :-)